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Helix geometry in proteins.

D J Barlow1, J M Thornton

  • 1Department of Crystallography, Birkbeck College London, U.K.

Journal of Molecular Biology
|June 5, 1988
PubMed
Summary
This summary is machine-generated.

Protein structures contain numerous alpha-helices and 3(10)-helices that deviate from ideal linear forms. Helix curvature and kinks, often caused by proline residues, may hold structural and functional significance.

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Area of Science:

  • Structural biology
  • Protein structure analysis
  • Bioinformatics

Background:

  • Protein secondary structures, including alpha-helices and 3(10)-helices, are fundamental to protein architecture.
  • Understanding helix conformations and deviations is crucial for predicting protein function and interactions.

Purpose of the Study:

  • To survey and analyze helix conformations in known protein crystal structures.
  • To characterize distortions in alpha-helices and identify factors contributing to these deviations.

Main Methods:

  • General survey of helices in 57 protein crystal structures.
  • Detailed analysis of 48 alpha-helices from 16 high-resolution structures.
  • Utilized a computer program (HBEND) to quantify helix distortions.

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Main Results:

  • Identified 291 alpha-helices and 71 3(10)-helices; no pi-helices observed.
  • Observed significant deviations from ideal linear helix conformations, with mean phi, psi angles differing from theoretical values.
  • Classified alpha-helices: 15% linear, 17% kinked, 58% curved.
  • Helix curvature attributed to hydrogen bonding patterns and packing constraints.
  • Proline-induced kinks (approx. 26 degrees) showed minimal hydrogen bond disruption and conserved residues, suggesting functional importance.

Conclusions:

  • Protein helices exhibit significant conformational variability compared to ideal models.
  • Helix distortions, particularly proline-induced kinks, are prevalent and potentially functionally relevant.
  • The study provides a quantitative characterization of helix conformations and distortions in proteins.